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- EMDB-39885: EmrAB-TolC MFS-type tripartite multidrug efflux pump FA -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-39885
TitleEmrAB-TolC MFS-type tripartite multidrug efflux pump FA
Map data
Sample
  • Complex: EmrABTolC
    • Protein or peptide: Multidrug export protein EmrA
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Multidrug export protein EmrB
KeywordsMultidrug efflux pump / MFS / EmrAB / STRUCTURAL PROTEIN
Function / homology
Function and homology information


MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / response to steroid hormone / bile acid and bile salt transport ...MacAB-TolC complex / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / response to steroid hormone / bile acid and bile salt transport / porin activity / monoatomic ion channel activity / efflux transmembrane transporter activity / transmembrane transporter activity / xenobiotic transmembrane transporter activity / cell outer membrane / response to toxic substance / transmembrane transport / outer membrane-bounded periplasmic space / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Drug resistance transporter EmrB-like / Efflux pump membrane protein / : / Type I secretion outer membrane protein, TolC / : / Cation efflux system protein CusB, domain 1 / : / RND efflux pump, membrane fusion protein, barrel-sandwich domain / : / Outer membrane efflux protein ...Drug resistance transporter EmrB-like / Efflux pump membrane protein / : / Type I secretion outer membrane protein, TolC / : / Cation efflux system protein CusB, domain 1 / : / RND efflux pump, membrane fusion protein, barrel-sandwich domain / : / Outer membrane efflux protein / Outer membrane efflux protein / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Outer membrane protein TolC / Multidrug export protein EmrB / Multidrug export protein EmrA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsDu D / Zhong Z / Tuerxunjiang M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971133 China
CitationJournal: To Be Published
Title: EmrAB-TolC MFS-type tripartite multidrug efflux pump FA
Authors: Du D / Zhong Z / Tuerxunjiang M
History
DepositionApr 25, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39885.png

Downloads & links

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Map

FileDownload / File: emd_39885.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.010257552 - 1.9646394
Average (Standard dev.)0.0009858945 (±0.022957435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39885_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39885_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_39885_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : EmrABTolC

EntireName: EmrABTolC
Components
  • Complex: EmrABTolC
    • Protein or peptide: Multidrug export protein EmrA
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Multidrug export protein EmrB

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Supramolecule #1: EmrABTolC

SupramoleculeName: EmrABTolC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Multidrug export protein EmrA

MacromoleculeName: Multidrug export protein EmrA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 43.977988 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MSANAETQTP QQPVKKSGKR KRLLLLLTLL FIIIAVAIGI YWFLVLRHFE ETDDAYVAGN QIQIMSQVSG SVTKVWADNT DFVKEGDVL VTLDPTDARQ AFEKAKTALA SSVRQTHQLM INSKQLQANI EVQKIALAKA QSDYNRRVPL GNANLIGREE L QHARDAVT ...String:
MSANAETQTP QQPVKKSGKR KRLLLLLTLL FIIIAVAIGI YWFLVLRHFE ETDDAYVAGN QIQIMSQVSG SVTKVWADNT DFVKEGDVL VTLDPTDARQ AFEKAKTALA SSVRQTHQLM INSKQLQANI EVQKIALAKA QSDYNRRVPL GNANLIGREE L QHARDAVT SAQAQLDVAI QQYNANQAMI LGTKLEDQPA VQQAATEVRN AWLALERTRI ISPMTGYVSR RAVQPGAQIS PT TPLMAVV PATNMWVDAN FKETQIANMR IGQPVTITTD IYGDDVKYTG KVVGLDMGTG SAFSLLPAQN ATGNWIKVVQ RLP VRIELD QKQLEQYPLR IGLSTLVSVN TTNRDGQVLA NKVRSTPVAV STAREISLAP VNKLIDDIVK ANAGGGSDYK DDDD K

UniProtKB: Multidrug export protein EmrA

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Macromolecule #2: Multidrug export protein EmrB

MacromoleculeName: Multidrug export protein EmrB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 67.336273 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MGMTPLADLE DNWETLNDNL KVIEKADNAA QVKDALTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRHG FDILVGQIDD ALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLERARSTL MAQLVIMTIA LSLATFMQVL DSTIANVAIP TIAGNLGSSL S QGTWVITS ...String:
MGMTPLADLE DNWETLNDNL KVIEKADNAA QVKDALTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRHG FDILVGQIDD ALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLERARSTL MAQLVIMTIA LSLATFMQVL DSTIANVAIP TIAGNLGSSL S QGTWVITS FGVANAISIP LTGWLAKRVG EVKLFLWSTI AFAIASWACG VSSSLNMLIF FRVIQGIVAG PLIPLSQSLL LN NYPPAKR SIALALWSMT VIVAPICGPI LGGYISDNYH WGWIFFINVP IGVAVVLMTL QTLRGRETRT ERRRIDAVGL ALL VIGIGS LQIMLDRGKE LDWFSSQEII ILTVVAVVAI CFLIVWELTD DNPIVDLSLF KSRNFTIGCL CISLAYMLYF GAIV LLPQL LQEVYGYTAT WAGLASAPVG IIPVILSPII GRFAHKLDMR RLVTFSFIMY AVCFYWRAYT FEPGMDFGAS AWPQF IQGF AVACFFMPLT TITLSGLPPE RLAAASSLSN FTRTLAGSIG TSITTTMWTN RESMHHAQLT ESVNPFNPNA QAMYSQ LEG LGMTQQQASG WIAQQITNQG LIISANEIFW MSAGIFLVLL GLVWFAKPPF G

UniProtKB: Multidrug export protein EmrB

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Macromolecule #3: Outer membrane protein TolC

MacromoleculeName: Outer membrane protein TolC / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 54.794344 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MKKLLPILIG LSLSGFSSLS QAENLMQVYQ QARLSNPELR KSAADRDAAF EKINEARSPL LPQLGLGADY TYSNGYRDAN GINSNATSA SLQLTQSIFD MSKWRALTLQ EKAAGIQDVT YQTDQQTLIL NTATAYFNVL NAIDVLSYTQ AQKEAIYRQL D QTTQRFNV ...String:
MKKLLPILIG LSLSGFSSLS QAENLMQVYQ QARLSNPELR KSAADRDAAF EKINEARSPL LPQLGLGADY TYSNGYRDAN GINSNATSA SLQLTQSIFD MSKWRALTLQ EKAAGIQDVT YQTDQQTLIL NTATAYFNVL NAIDVLSYTQ AQKEAIYRQL D QTTQRFNV GLVAITDVQN ARAQYDTVLA NELTARNNLD NAVEQLRQIT GNYYPELAAL NVENFKTDKP QPVNALLKEA EK RNLSLLQ ARLSQDLARE QIRQAQDGHL PTLDLTASTG ISDTSYSGSK TRGAAGTQYD DSNMGQNKVG LSFSLPIYQG GMV NSQVKQ AQYNFVGASE QLESAHRSVV QTVRSSFNNI NASISSINAY KQAVVSAQSS LDAMEAGYSV GTRTIVDVLD ATTT LYNAK QELANARYNY LINQLNIKSA LGTLNEQDLL ALNNALSKPV STNPENVAPQ TPEQNAIADG YAPDSPAPVV QQTSA RTTT SNGHNPFRND YKDDDDK

UniProtKB: Outer membrane protein TolC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/HE
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18440
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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